Date: 2018-08-17
R version: 3.5.0
Corresponding author: matthew.malishev@gmail.com
This document can be found at https://github.com/darwinanddavis/SchistoMesocosm

Follow instructions in code chunks labelled ‘fileoutput’ to toggle pdf of plots saved to directory on/off (‘Size_per_tank_over_time.pdf’)

TO DO

  • How much of the population does the sampling effort capture?
  • Scale diameter densities per tank over time to upper limit of each tank (set ylim to highest value for each tank)
  • Scale diameter densities per tank over time to upper limit of all tanks (set ylim to highest value for all tanks)
  • Split plots by line color code showing point where snails are reproductive viable (8 mm and above).
  • Which tanks and conditions reach reproductive size?
  • Replot by size class and resource combo e.g. low resources and small size class v low resources and large size class

Overview

This document uses the schisto mesocosm 2016 data to explore cercariae production from snail hosts of different body sizes (diameter in mm and mass in mg) over a 14 week period under high and low N/P nutrient conditions. Host reproduction (egg masses) is also calculated.

Install dependencies

Get data

wd <- params$dir # working dir is set in yaml header
setwd(paste0(wd,"/"))
f <- "meso1_.csv"
f2 <- "meso2_.csv"

Load data

'data.frame':   720 obs. of  13 variables:
 $ Tank                : int  1 2 3 4 5 6 7 8 9 10 ...
 $ NP                  : chr  "High" "Low" "Low" "High" ...
 $ Size                : chr  "Small" "Intermediate" "Intermediate" "Small" ...
 $ Schisto             : chr  "No" "Yes" "Yes" "Yes" ...
 $ Week                : int  0 0 0 0 0 0 0 0 0 0 ...
 $ Snail               : int  60 60 60 60 60 60 60 60 60 60 ...
 $ Total_Biomass       : num  96 620.6 670.5 86.7 121.4 ...
 $ Cercarial_production: int  0 0 0 0 0 0 0 0 0 0 ...
 $ Infected_abundance  : int  0 0 0 0 0 0 0 0 0 0 ...
 $ Sampling_Effort     : int  NA NA NA NA NA NA NA NA NA NA ...
 $ Eggs                : int  NA NA NA NA NA NA NA NA NA NA ...
 $ Phyto_F             : num  NA NA NA NA NA NA NA NA NA NA ...
 $ Peri_F              : num  NA NA NA NA NA NA NA NA NA NA ...

Set plotting graphics

Set plotting parameters

Get only infected snails

 

Mesocosm 1 data sheet

Snail size per tank

Shell diameter (mm) per tank


    Welch Two Sample t-test

data:  Diameter and Tank
t = -292.67, df = 54609, p-value < 2.2e-16
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -19.45879 -19.19989
sample estimates:
mean of x mean of y 
 5.821956 25.151292

Snail diameter (mm) distribution

  xchar= 0.7875 ; (yextra,ychar)= -0.004785 0.004785 
  points2( 30.85 30.85 , 0.1 0.09522 , pch= 20 20 , ...)

Snail size over time (weeks)

Shell diameter (mm) over time (weeks)
~1000 eggs inoculated at 0,2,4,6 weeks

Snail size over time (weeks) per tank

For all tanks (n = 48), see ‘Size_per_tank_over_time.pdf’   in /Users/malishev/Documents/Emory/research/mesocosm

  ~1000 eggs inoculated at 0,2,4,6 weeks

Select tank. Max 48

tank <- 12 # Select tank #. Max 48   
paste0("Tank ",tank) 
[1] "Tank 12"

Snail size over time (weeks) per tank (High resources)

  See “Size_per_tank_over_time_HIGH.pdf”   in /Users/malishev/Documents/Emory/research/mesocosm

Snail size over time (weeks) per tank (Low resources)

  See “Size_per_tank_over_time_LOW.pdf”   in /Users/malishev/Documents/Emory/research/mesocosm

Large snails over time (weeks) per tank (High resources)

  See “Size_per_tank_over_time_HIGH_LARGE.pdf”   in /Users/malishev/Documents/Emory/research/mesocosm

Large snails over time (weeks) per tank (low resources)

  See “Size_per_tank_over_time_LOW_LARGE.pdf”   in /Users/malishev/Documents/Emory/research/mesocosm

Small snails over time (weeks) per tank (High resources)

  See “Size_per_tank_over_time_HIGH_SMALL.pdf”   in /Users/malishev/Documents/Emory/research/mesocosm

Small snails over time (weeks) per tank (low resources)

  See “Size_per_tank_over_time_LOW_SMALL.pdf”   in /Users/malishev/Documents/Emory/research/mesocosm

Body mass (mg) over time (weeks)

(Soft tissue dry mass in mg = 0.0096 * Diameter[in mm]^3)
~1000 eggs inoculated at 0,2,4,6 weeks

      Biomass Cercariae
6469 244.7544         0

Without max value of as.numeric(outer)[1]

Snail size and number of cercariae produced

Point size by cercariae number
Linear log

Snail mass and cercariae produced (mg)

Snail size per tank

Shell diameter (mm)
Select tank. Max 48

[1] "Tank 24"

Cercariae production over time

Cercariae shed over 90 mins per week
~1000 eggs inoculated at 0,2,4,6 weeks
Snail abundance over time (weeks)

Tank cercariae production over time per tank

Select tank. Max 48

[1] "Tank 24"
[1] 2300

Mesocosm 2 data sheet

Egg mass distribution

N/P concentration v egg mass

Phyto and Peri Distribution

phyto = flourescence units
peri = flourescence per 2 weeks / 3.5 inch^2 tile (gross productivity biomass rate)

Egg Mass over time v presence of schisto

~1000 eggs inoculated at 0,2,4,6 weeks

Size class vs Egg mass (with schisto)

  xchar= 3.937 ; (yextra,ychar)= -0.001435 0.001435 
  points2( 147.7 147.7 147.7 , 0.03072 0.02928 0.02785 , pch= 20 20 20 , ...)

Egg Mass over time (weeks)

~1000 eggs inoculated at 0,2,4,6 weeks